Mouse chromosomes are being sorted to identify centromere specific proteins. Sorting to recover heterochromatic enriched proteins from mouse micro-chromosomes has been accomplished. 2-D gel analysis is being used to separate the proteins from the flow sorted micro-chromosomes. Multiple experiments have been performed to determine the level of protein cross-linking caused by the lasers used to excite the two fluorochromes. If there is successful protein cross-linking this technique could be extended to other applications.